Mercurial > repos > jjohnson > snpeff
changeset 13:4be8e0068bc3
Update loc data to separate version 4 databases
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 21 Oct 2014 14:05:27 -0500 |
parents | 6d429d880a75 |
children | 4511f153078c |
files | snpEff.xml tool-data/snpeff4_annotations.loc.sample tool-data/snpeff4_databases.loc.sample tool-data/snpeff4_genomedb.loc.sample tool-data/snpeff4_regulationdb.loc.sample tool-data/snpeff_annotations.loc.sample tool-data/snpeff_databases.loc.sample tool-data/snpeff_genomedb.loc.sample tool-data/snpeff_regulationdb.loc.sample tool_data_table_conf.xml.sample |
diffstat | 10 files changed, 31 insertions(+), 31 deletions(-) [+] |
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--- a/snpEff.xml Mon Oct 20 08:37:01 2014 -0500 +++ b/snpEff.xml Tue Oct 21 14:05:27 2014 -0500 @@ -94,20 +94,20 @@ <when value="cached"> <param name="genomeVersion" type="select" label="Genome"> <!--GENOME DESCRIPTION--> - <options from_data_table="snpeff_genomedb"> + <options from_data_table="snpeff4_genomedb"> <filter type="unique_value" column="0" /> </options> </param> <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> <help>These are available for only a few genomes</help> - <options from_data_table="snpeff_annotations"> + <options from_data_table="snpeff4_annotations"> <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> <filter type="unique_value" column="1" /> </options> </param> <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> <help>These are available for only a few genomes</help> - <options from_data_table="snpeff_regulationdb"> + <options from_data_table="snpeff4_regulationdb"> <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> <filter type="unique_value" column="1" /> </options> @@ -130,7 +130,7 @@ </param> </when> <when value="named"> - <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/> + <param name="genome_version" type="text" value="GRCh38.76" label="Snpff Version Name"/> </when> </conditional>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeff4_annotations.loc.sample Tue Oct 21 14:05:27 2014 -0500 @@ -0,0 +1,5 @@ +## Regulation Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +#genome annotation_name description +#GRCh37.71 nextprot nextprot +#GRCh37.71 motif motif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeff4_databases.loc.sample Tue Oct 21 14:05:27 2014 -0500 @@ -0,0 +1,5 @@ +## Available Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +## the Description field in this sample is "Genome : Version" +#Version Description +#GRCh37.68 Homo sapiens : GRCh37.68
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeff4_genomedb.loc.sample Tue Oct 21 14:05:27 2014 -0500 @@ -0,0 +1,5 @@ +## Downloaded Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +## the Description field in this sample is "Genome : Version" +#Version Description data_dir path +#GRCh37.68 Homo sapiens : GRCh37.68 /home/galaxy/snpEff/data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeff4_regulationdb.loc.sample Tue Oct 21 14:05:27 2014 -0500 @@ -0,0 +1,4 @@ +## Regulation Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +#genome regulation_name description +#GRCh37.70 CD4 CD4
--- a/tool-data/snpeff_annotations.loc.sample Mon Oct 20 08:37:01 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -## Regulation Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -#genome annotation_name description -#GRCh37.71 nextprot nextprot -#GRCh37.71 motif motif
--- a/tool-data/snpeff_databases.loc.sample Mon Oct 20 08:37:01 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -## Available Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -## the Description field in this sample is "Genome : Version" -#Version Description -#GRCh37.68 Homo sapiens : GRCh37.68
--- a/tool-data/snpeff_genomedb.loc.sample Mon Oct 20 08:37:01 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -## Downloaded Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -## the Description field in this sample is "Genome : Version" -#Version Description data_dir path -#GRCh37.68 Homo sapiens : GRCh37.68 /home/galaxy/snpEff/data
--- a/tool-data/snpeff_regulationdb.loc.sample Mon Oct 20 08:37:01 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -## Regulation Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -#genome regulation_name description -#GRCh37.70 CD4 CD4
--- a/tool_data_table_conf.xml.sample Mon Oct 20 08:37:01 2014 -0500 +++ b/tool_data_table_conf.xml.sample Tue Oct 21 14:05:27 2014 -0500 @@ -1,19 +1,19 @@ <tables> - <table name="snpeff_databases" comment_char="#"> + <table name="snpeff4_databases" comment_char="#"> <columns>value, name</columns> - <file path="tool-data/snpeff_databases.loc" /> + <file path="tool-data/snpeff4_databases.loc" /> </table> - <table name="snpeff_genomedb" comment_char="#"> + <table name="snpeff4_genomedb" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/snpeff_genomedb.loc" /> + <file path="tool-data/snpeff4_genomedb.loc" /> </table> - <table name="snpeff_regulationdb" comment_char="#"> + <table name="snpeff4_regulationdb" comment_char="#"> <columns>genome, value, name</columns> - <file path="tool-data/snpeff_regulationdb.loc" /> + <file path="tool-data/snpeff4_regulationdb.loc" /> </table> - <table name="snpeff_annotations" comment_char="#"> + <table name="snpeff4_annotations" comment_char="#"> <columns>genome, value, name</columns> - <file path="tool-data/snpeff_annotations.loc" /> + <file path="tool-data/snpeff4_annotations.loc" /> </table> </tables>